Updated: Fri Jan 9 18:09:32 2015

DMR identification with methyl_diff

Background


UMR summary and sanity check

Sample Total.DMR Hyper.DMR Hypo.DMR
Cortex-HuFNSC02_Cortex-HuFNSC04 1283 179 1104
GE-HuFNSC02_GE-HuFNSC04 3002 722 2280

UMR asymmetry

GREAT enrichment for GW-associated UMRs

UMR Genomic breakdown

Proximal UMRs and DE genes

proximal.DMRs unique.genes DE.DMRs unique.DE.genes same.direction
Cortex04.UMRs 7 7 0 0 0
Cortex02.UMRs 215 215 24 19 21
GE04.UMRs 37 36 6 5 3
GE02.UMRs 402 402 64 57 49

Proximal 13-week UMRs in both Cortex and GE

id name description
ENSG00000189334 S100A14 S100_calcium_binding_protein_A14_[Source:HGNC_Symbol;Acc:18901]
ENSG00000237693 IRGM immunity-related_GTPase_family,M[Source:HGNC_Symbol;Acc:29597]
ENSG00000124564 SLC17A3 solute_carrier_family_17_(sodium_phosphate),member3_[Source:HGNC_Symbol;Acc:10931]

Proximal GE 13-week UMRs with DE genes

id name description DM DE
ENSG00000134954 ETS1 v-ets_erythroblastosis_virus_E26_oncogene_homolog_1_(avian)_[Source:HGNC_Symbol;Acc:3488] hyper UP
ENSG00000136352 NKX2-1 NK2_homeobox_1_[Source:HGNC_Symbol;Acc:11825] hyper UP
ENSG00000165588 OTX2 orthodenticle_homeobox_2_[Source:HGNC_Symbol;Acc:8522] hyper UP
ENSG00000231421 hyper DN
ENSG00000155760 FZD7 frizzled_family_receptor_7_[Source:HGNC_Symbol;Acc:4045] hyper DN

Proximal 17-week UMRs with DE genes in both Cortex and GE

id name description DM DE
ENSG00000255737 NA HCG2014417,isoformCRA_aUncharacterized_proteincDNA_FLJ59598_[Source:UniProtKB/TrEMBL;Acc:B7Z718] hypo UP
ENSG00000167178 ISLR2 immunoglobulin_superfamily_containing_leucine-rich_repeat_2_[Source:HGNC_Symbol;Acc:29286] hypo UP
ENSG00000161999 JMJD8 jumonji_domain_containing_8_[Source:HGNC_Symbol;Acc:14148] hypo UP
ENSG00000051523 CYBA cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577] hypo UP
ENSG00000169515 CCDC8 coiled-coil_domain_containing_8_[Source:HGNC_Symbol;Acc:25367] hypo UP
ENSG00000205927 OLIG2 oligodendrocyte_lineage_transcription_factor_2_[Source:HGNC_Symbol;Acc:9398] hypo UP
ENSG00000189060 H1F0 H1_histone_family,member0_[Source:HGNC_Symbol;Acc:4714] hypo UP
ENSG00000146904 EPHA1 EPH_receptor_A1_[Source:HGNC_Symbol;Acc:3385] hypo UP
ENSG00000165072 MAMDC2 MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673] hypo UP

UMRs overlapping with TFBS

TF UMR17week_Cortex UMR13week_Cortex Ratio_Cortex UMR17week_GE UMR13week_GE Ratio_GE
MAZ 133 5 26.6000 319 12 26.5833
GTF2F1 28 1 28.0000 103 2 51.5000
ZBTB7A 97 3 32.3333 201 3 67.0000
HMGN3 66 2 33.0000 131 4 32.7500
NRF1 34 1 34.0000 64 1 64.0000
MXI1 112 3 37.3333 262 7 37.4286
E2F4 50 1 50.0000 110 1 110.0000
CCNT2 87 1 87.0000 148 4 37.0000
E2F6 140 1 140.0000 263 8 32.8750

UMR enrichment at chromosome ends

DE genes summary

UP DN DE GW type Sample
1 284 281 565 GW17-GW15 cortex GW17-GW15.1_cortex
2 365 165 530 GW17-GW13 cortex GW17-GW13.1_cortex
3 398 283 681 GW17-GW15 cortex GW17-GW15.2_cortex
4 497 225 722 GW17-GW13 cortex GW17-GW13.2_cortex
5 459 183 642 GW15-GW13 cortex GW15-GW13_cortex
6 587 274 861 GW17-GW15 GE GW17-GW15.1_GE
7 645 238 883 GW17-GW13 GE GW17-GW13.1_GE
8 609 312 921 GW17-GW15 GE GW17-GW15.2_GE
9 610 259 869 GW17-GW13 GE GW17-GW13.2_GE
10 313 232 545 GW15-GW13 GE GW15-GW13_GE
11 74 75 173 GW17-GW15 shared GW17-GW15.1_shared
12 239 65 311 GW17-GW13 shared GW17-GW13.1_shared
13 78 75 180 GW17-GW15 shared GW17-GW15.2_shared
14 282 84 372 GW17-GW13 shared GW17-GW13.2_shared
15 79 74 166 GW15-GW13 shared GW15-GW13_shared

Stage-specific DE gene profiles

  • Cortex stage-specific DE genes are mostly turned on during GW13-GW15, while GE stage-specific DE genes are mostly turned on during GW15-GW17. This supports the clustering in coding gene RPKM, exon RPKM and miRNA RPM that in cortex GW15 clustered with GW17, and in GE GW15 clustered with GW13.

Genes activated during GW13-GW15 in cortex

  • ALX3: a transcriptional regulator involved in cell-type differentiation and development. Preferential methylation of this genes promoter is associated with advanced-stage neuroblastoma tumors.
  • EPHB2: mediate numerous developmental processes, particularly in the nervous system. Functions in axon guidance during development.
  • FAT2: This protein most likely functions as a cell adhesion molecule, controlling cell proliferation and playing an important role in cerebellum development.
  • FOSL1: regulators of cell proliferation, differentiation, and transformation. associated with glioblastoma multiforme.
  • HNF1A: sequence-specific DNA binding transcription factor activity.
  • LHX4: a transcription factor involved in the control of differentiation and development of the pituitary gland.
  • MEIS2: essential contributors to developmental programs.
  • POU5F1: controls the expression of a number of genes involved in embryonic development such as YES1, FGF4, UTF1 and ZFP206. Critical for early embryogenesis and for embryonic stem cell pluripotency.
  • CDR1: found in some patients with paraneoplastic cerebellar degeneration.
  • CCKAR: modulates feeding and dopamine-induced behavior in the central and peripheral nervous system.
  • FOXH1: Transcriptional activator.
  • LGI1: is rearranged as a result of translocations in glioblastoma cell lines. May play a role in the control of neuroblastoma cell survival.
  • LHFPL5: In the inner ear, may be a component of the hair cells mechanotransduction machinery.
  • NEGR1: involved in cell-adhesion. May function as a trans-neural growth-promoting factor in regenerative axon sprouting in the mammalian brain.
  • NRP2: may play a role in cardiovascular development, axon guidance, and tumorigenesis.
  • OLIG2: an essential regulator of ventral neuroectodermal progenitor cell fate.
  • RTN1: May be involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells. a specific marker for neurological diseases and cancer.

Genes activated during GW15-GW17 in GE

  • ALX3: a transcriptional regulator involved in cell-type differentiation and development. Preferential methylation of this genes promoter is associated with advanced-stage neuroblastoma tumors.
  • EPHB3: mediate numerous developmental processes, particularly in the nervous system. Functions in axon guidance during development.
  • GPR98: a G-protein coupled receptor that may have an important role in the development of the central nervous system.
  • GSX1: Homeobox transcription factor that plays an important role in pituitary development.
  • HNF1A: sequence-specific DNA binding transcription factor activity.
  • LHX4: a transcription factor involved in the control of differentiation and development of the pituitary gland.
  • LHX6: a transcription factor required for the expression of a subset of genes involved in interneurons migration and development.
  • NKX2-1: a Homeobox transcription factor that activates thyroid specific genes.
  • SATB2: a Homeobox transcription factor and regulatory determinant of corticocortical connections in the developing cerebral cortex.
  • SIX3: a Homeobox transcription factor that plays a role in eye development.
  • SLITRK1: Enhances neurite outgrowth.
  • SLITRK4: suppress neurite outgrowth.
  • SLITRK5: suppress neurite outgrowth.
  • CDR1: found in some patients with paraneoplastic cerebellar degeneration.
  • CHAT: a characteristic feature of cholinergic neurons, and changes in these neurons may explain some of the symptoms of Alzheimers disease.
  • DCC: Receptor for netrin required for axon guidance. Mediates axon attraction of neuronal growth cones in the developing nervous system upon ligand binding.
  • FOXH1: Transcriptional activator.
  • FOXP4: forkhead box (FOX) transcription factor.
  • FZD5: Interacts specifically with Wnt5A to induce the beta-catenin pathway.
  • INA: a member of the intermediate filament family and is involved in the morphogenesis of neurons.
  • IRX2: a member of the Iroquois homeobox gene family. Members of this family appear to play multiple roles during pattern formation of vertebrate embryos.
  • NTN1: netrin is thought to be involved in axon guidance and cell migration during development.
  • NXPH1: forms a very tight complex with alpha neurexins, a group of proteins that promote adhesion between dendrites and axons.
  • NRGN: a direct target for thyroid hormone in human brain, and that control of expression of this gene could underlay many of the consequences of hypothyroidism on mental states during development.
  • NRP2: may play a role in cardiovascular development, axon guidance, and tumorigenesis.
  • OLFM1: May play an important role in regulating the production of neural crest cells by the neural tube.
  • OLFM3: May play an important role in regulating the production of neural crest cells by the neural tube.
  • OLIG2: an essential regulator of ventral neuroectodermal progenitor cell fate.
  • LPPR4: is located in the membranes of outgrowing axons and has been shown to be important for axonal outgrowth during development and regenerative sprouting.
  • PLXNA2: semaphorin co-receptors. Semaphorins are a large family of secreted or membrane-bound proteins that mediate repulsive effects on axon pathfinding during nervous system development.
  • SFRP1: soluble modulators of Wnt signaling; epigenetic silencing of SFRP genes leads to deregulated activation of the Wnt-pathway which is associated with cancer.
  • SLIT1: During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions.
  • SLIT2: SLIT1 and SLIT2 together seem to be essential for midline guidance in the forebrain by acting as repulsive signal preventing inappropriate midline crossing by axons projecting from the olfactory bulb.
  • STMN2: plays a regulatory role in neuronal growth and is also thought to be involved in osteogenesis. Reductions in the expression of this gene have been associated with Downs syndrome and Alzheimers disease.
  • VAX1: homeobox transcription factors that may play an important role in the development of anterior ventral forebrain and visual system.
  • WNT7A: have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis.
  • WNT5A: Stimulates cell migration. Decreases proliferation, migration, invasiveness and clonogenicity of carcinoma cells and may act as a tumor suppressor. Mediates motility of melanoma cells. Required during embryogenesis for extension of the primary anterior-posterior axis and for outgrowth of limbs and the genital tubercle.

Stage-specific DE gene shared by Crotex and GE

  1. GW13-15:UP, GW15-17:UP;
    No genes
  2. GW13-15:UP, GW15-17:DN;
    id name description
    ENSG00000168542 COL3A1 collagen,typeIII,alpha1_[Source:HGNC_Symbol;Acc:2201]
    ENSG00000133636 NTS neurotensin_[Source:HGNC_Symbol;Acc:8038]
    ENSG00000066032 CTNNA2 catenin_(cadherin-associated_protein),alpha2_[Source:HGNC_Symbol;Acc:2510]
    ENSG00000135063 FAM189A2 family_with_sequence_similarity_189,memberA2_[Source:HGNC_Symbol;Acc:24820]
    ENSG00000214401
    ENSG00000099984 GSTT2 glutathione_S-transferase_theta_2_[Source:HGNC_Symbol;Acc:4642]
    ENSG00000238083 LRRC37A2 leucine_rich_repeat_containing_37,memberA2_[Source:HGNC_Symbol;Acc:32404]
    ENSG00000101255 TRIB3 tribbles_homolog_3_(Drosophila)_[Source:HGNC_Symbol;Acc:16228]
    ENSG00000160284 C21orf56 chromosome_21_open_reading_frame_56_[Source:HGNC_Symbol;Acc:1298]
  3. GW13-15:DN, GW15-17:UP;
    id name description
    ENSG00000022556 NLRP2 NLR_family,pyrindomain_containing_2_[Source:HGNC_Symbol;Acc:22948]
    ENSG00000225607 NA Uncharacterized_proteincDNA_FLJ60024,highlysimilar_to_Cytochrome_P450_4F12__[Source:UniProtKB/TrEMBL;Acc:B4DNA9]
    ENSG00000147813 NAPRT1 nicotinate_phosphoribosyltransferase_domain_containing_1_[Source:HGNC_Symbol;Acc:30450]
    ENSG00000167654 ATCAY ataxia,cerebellar,Cayman_type_[Source:HGNC_Symbol;Acc:779]
  4. GW13-15:DN, GW15-17:DN;
    No genes
  5. GW13-15:UP, GW15-17:not DE;
    id name description
    ENSG00000149054 ZNF215 zinc_finger_protein_215_[Source:HGNC_Symbol;Acc:13007]
    ENSG00000215845 TSTD1 thiosulfate_sulfurtransferase_(rhodanese)-like_domain_containing_1_[Source:HGNC_Symbol;Acc:35410]
    ENSG00000100336 APOL4 apolipoprotein_L,4[Source:HGNC_Symbol;Acc:14867]
    ENSG00000163823 CCR1 chemokine_(C-C_motif)receptor1_[Source:HGNC_Symbol;Acc:1602]
    ENSG00000169220 RGS14 regulator_of_G-protein_signaling_14_[Source:HGNC_Symbol;Acc:9996]
    ENSG00000203804 C1orf138 chromosome_1_open_reading_frame_138_[Source:HGNC_Symbol;Acc:32041]
    ENSG00000204520 MICA MHC_class_I_polypeptide-related_sequence_A_[Source:HGNC_Symbol;Acc:7090]
    ENSG00000080573 COL5A3 collagen,typeV,alpha3_[Source:HGNC_Symbol;Acc:14864]
    ENSG00000165379 LRFN5 leucine_rich_repeat_and_fibronectin_type_III_domain_containing_5_[Source:HGNC_Symbol;Acc:20360]
    ENSG00000213402 PTPRCAP protein_tyrosine_phosphatase,receptortype,C-associatedprotein_[Source:HGNC_Symbol;Acc:9667]
    ENSG00000139155 SLCO1C1 solute_carrier_organic_anion_transporter_family,member1C1_[Source:HGNC_Symbol;Acc:13819]
    ENSG00000187773 FAM69C family_with_sequence_similarity_69,memberC_[Source:HGNC_Symbol;Acc:31729]
    ENSG00000133216 EPHB2 EPH_receptor_B2_[Source:HGNC_Symbol;Acc:3393]
    ENSG00000119737 GPR75 G_protein-coupled_receptor_75_[Source:HGNC_Symbol;Acc:4526]
    ENSG00000126790 C14orf149 chromosome_14_open_reading_frame_149_[Source:HGNC_Symbol;Acc:20488]
    ENSG00000162733 DDR2 discoidin_domain_receptor_tyrosine_kinase_2_[Source:HGNC_Symbol;Acc:2731]
    ENSG00000108231 LGI1 leucine-rich,gliomainactivated_1_[Source:HGNC_Symbol;Acc:6572]
    ENSG00000161921 CXCL16 chemokine_(C-X-C_motif)ligand16_[Source:HGNC_Symbol;Acc:16642]
    ENSG00000119673 ACOT2 acyl-CoA_thioesterase_2_[Source:HGNC_Symbol;Acc:18431]
    ENSG00000135046 ANXA1 annexin_A1_[Source:HGNC_Symbol;Acc:533]
    ENSG00000215790 SLC35E2 solute_carrier_family_35,memberE2_[Source:HGNC_Symbol;Acc:20863]
    ENSG00000157150 TIMP4 TIMP_metallopeptidase_inhibitor_4_[Source:HGNC_Symbol;Acc:11823]
    ENSG00000170579 DLGAP1 discs,large(Drosophila)homolog-associatedprotein_1_[Source:HGNC_Symbol;Acc:2905]
    ENSG00000143252 SDHC succinate_dehydrogenase_complex,subunitC,integralmembrane_protein,15kDa[Source:HGNC_Symbol;Acc:10682]
    ENSG00000107796 ACTA2 actin,alpha2,smoothmuscle,aorta[Source:HGNC_Symbol;Acc:130]
    ENSG00000124193 SRSF6 serine/arginine-rich_splicing_factor_6_[Source:HGNC_Symbol;Acc:10788]
    ENSG00000152661 GJA1 gap_junction_protein,alpha1,43kDa[Source:HGNC_Symbol;Acc:4274]
    ENSG00000184110 EIF3C eukaryotic_translation_initiation_factor_3,subunitC_[Source:HGNC_Symbol;Acc:3279]
  6. GW13-15:DN, GW15-17:not DE;
    id name description
    ENSG00000166923 GREM1 gremlin_1_[Source:HGNC_Symbol;Acc:2001]
    ENSG00000164123 C4orf45 chromosome_4_open_reading_frame_45_[Source:HGNC_Symbol;Acc:26342]
    ENSG00000008196 TFAP2B transcription_factor_AP-2_beta_(activating_enhancer_binding_protein_2_beta)_[Source:HGNC_Symbol;Acc:11743]
    ENSG00000186897 C1QL4 complement_component_1,qsubcomponent-like_4_[Source:HGNC_Symbol;Acc:31416]
    ENSG00000054598 FOXC1 forkhead_box_C1_[Source:HGNC_Symbol;Acc:3800]
    ENSG00000104808 DHDH dihydrodiol_dehydrogenase_(dimeric)_[Source:HGNC_Symbol;Acc:17887]
    ENSG00000124813 RUNX2 runt-related_transcription_factor_2_[Source:HGNC_Symbol;Acc:10472]
    ENSG00000173068 BNC2 basonuclin_2_[Source:HGNC_Symbol;Acc:30988]
    ENSG00000165929 TC2N tandem_C2_domains,nuclear[Source:HGNC_Symbol;Acc:19859]
    ENSG00000157064 NMNAT2 nicotinamide_nucleotide_adenylyltransferase_2_[Source:HGNC_Symbol;Acc:16789]
    ENSG00000243244 STON1 stonin_1_[Source:HGNC_Symbol;Acc:17003]
    ENSG00000173809 TDRD12 tudor_domain_containing_12_[Source:HGNC_Symbol;Acc:25044]
    ENSG00000135333 EPHA7 EPH_receptor_A7_[Source:HGNC_Symbol;Acc:3390]
    ENSG00000231421
    ENSG00000168675 C18orf1 chromosome_18_open_reading_frame_1_[Source:HGNC_Symbol;Acc:1224]
    ENSG00000156395 SORCS3 sortilin-related_VPS10_domain_containing_receptor_3_[Source:HGNC_Symbol;Acc:16699]
    ENSG00000204103 MAFB v-maf_musculoaponeurotic_fibrosarcoma_oncogene_homolog_B_(avian)_[Source:HGNC_Symbol;Acc:6408]
    ENSG00000168447 SCNN1B sodium_channel,nonvoltage-gated1,beta[Source:HGNC_Symbol;Acc:10600]
    ENSG00000106546 AHR aryl_hydrocarbon_receptor_[Source:HGNC_Symbol;Acc:348]
    ENSG00000117598 NA Lipid_phosphate_phosphatase-related_protein_type_5_[Source:UniProtKB/Swiss-Prot;Acc:Q32ZL2]
    ENSG00000120322 PCDHB8 protocadherin_beta_8_[Source:HGNC_Symbol;Acc:8693]
    ENSG00000250305 NA Putative_methyltransferase_KIAA1456_[Source:UniProtKB/Swiss-Prot;Acc:Q9P272]
    ENSG00000106868 SUSD1 sushi_domain_containing_1_[Source:HGNC_Symbol;Acc:25413]
    ENSG00000183943 PRKX protein_kinase,X-linked[Source:HGNC_Symbol;Acc:9441]
    ENSG00000204060 FOXO6 forkhead_box_O6_[Source:HGNC_Symbol;Acc:24814]
    ENSG00000170941 NA Uncharacterized_protein_KIAA1456_[Source:UniProtKB/Swiss-Prot;Acc:Q8N9K7]
    ENSG00000063438 AHRR aryl-hydrocarbon_receptor_repressor_[Source:HGNC_Symbol;Acc:346]
    ENSG00000107902 LHPP phospholysine_phosphohistidine_inorganic_pyrophosphate_phosphatase_[Source:HGNC_Symbol;Acc:30042]
    ENSG00000169436 COL22A1 collagen,typeXXII,alpha1_[Source:HGNC_Symbol;Acc:22989]
    ENSG00000184985 SORCS2 sortilin-related_VPS10_domain_containing_receptor_2_[Source:HGNC_Symbol;Acc:16698]
    ENSG00000163328 GPR155 G_protein-coupled_receptor_155_[Source:HGNC_Symbol;Acc:22951]
    ENSG00000173598 NUDT4 nudix_(nucleoside_diphosphate_linked_moiety_X)-type_motif_4_[Source:HGNC_Symbol;Acc:8051]
    ENSG00000114200 BCHE butyrylcholinesterase_[Source:HGNC_Symbol;Acc:983]
    ENSG00000183722 LHFP lipoma_HMGIC_fusion_partner_[Source:HGNC_Symbol;Acc:6586]
    ENSG00000139722 VPS37B vacuolar_protein_sorting_37_homolog_B_(S.cerevisiae)[Source:HGNC_Symbol;Acc:25754]
  7. GW13-15:not DE, GW15-17:UP;
    id name description
    ENSG00000145247 OCIAD2 OCIA_domain_containing_2_[Source:HGNC_Symbol;Acc:28685]
    ENSG00000070748 CHAT choline_O-acetyltransferase_[Source:HGNC_Symbol;Acc:1912]
    ENSG00000165659 DACH1 dachshund_homolog_1_(Drosophila)_[Source:HGNC_Symbol;Acc:2663]
    ENSG00000165983 PTER phosphotriesterase_related_[Source:HGNC_Symbol;Acc:9590]
    ENSG00000139220 PPFIA2 protein_tyrosine_phosphatase,receptortype,fpolypeptide_(PTPRF),interactingprotein_(liprin),alpha2_[Source:HGNC_Symbol;Acc:9246]
    ENSG00000147255 IGSF1 immunoglobulin_superfamily,member1_[Source:HGNC_Symbol;Acc:5948]
    ENSG00000146233 CYP39A1 cytochrome_P450,family39,subfamilyA,polypeptide1_[Source:HGNC_Symbol;Acc:17449]
    ENSG00000181649 PHLDA2 pleckstrin_homology-like_domain,familyA,member2_[Source:HGNC_Symbol;Acc:12385]
    ENSG00000204516 MICB MHC_class_I_polypeptide-related_sequence_B_[Source:HGNC_Symbol;Acc:7091]
    ENSG00000164692 COL1A2 collagen,typeI,alpha2_[Source:HGNC_Symbol;Acc:2198]
    ENSG00000114805 PLCH1 phospholipase_C,eta1_[Source:HGNC_Symbol;Acc:29185]
    ENSG00000051523 CYBA cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577]
    ENSG00000145703 IQGAP2 IQ_motif_containing_GTPase_activating_protein_2_[Source:HGNC_Symbol;Acc:6111]
    ENSG00000165072 MAMDC2 MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673]
    ENSG00000130558 OLFM1 olfactomedin_1_[Source:HGNC_Symbol;Acc:17187]
    ENSG00000120318 ARAP3 ArfGAP_with_RhoGAP_domain,ankyrinrepeat_and_PH_domain_3_[Source:HGNC_Symbol;Acc:24097]
    ENSG00000198750 GATSL2 GATS_protein-like_2_[Source:HGNC_Symbol;Acc:37073]
    ENSG00000162849 KIF26B kinesin_family_member_26B_[Source:HGNC_Symbol;Acc:25484]
    ENSG00000134333 LDHA lactate_dehydrogenase_A_[Source:HGNC_Symbol;Acc:6535]
    ENSG00000064666 CNN2 calponin_2_[Source:HGNC_Symbol;Acc:2156]
  8. GW13-15:not DE, GW15-17:DN;
    id name description
    ENSG00000259210
    ENSG00000198650 TAT tyrosine_aminotransferase_[Source:HGNC_Symbol;Acc:11573]
    ENSG00000163053 SLC16A14 solute_carrier_family_16,member14_(monocarboxylic_acid_transporter_14)_[Source:HGNC_Symbol;Acc:26417]
    ENSG00000125637 PSD4 pleckstrin_and_Sec7_domain_containing_4_[Source:HGNC_Symbol;Acc:19096]
    ENSG00000153822 KCNJ16 potassium_inwardly-rectifying_channel,subfamilyJ,member16_[Source:HGNC_Symbol;Acc:6262]
    ENSG00000188803 SHISA6 shisa_homolog_6_(Xenopus_laevis)_[Source:HGNC_Symbol;Acc:34491]
    ENSG00000127952 STYXL1 serine/threonine/tyrosine_interacting-like_1_[Source:HGNC_Symbol;Acc:18165]
    ENSG00000150907 FOXO1 forkhead_box_O1_[Source:HGNC_Symbol;Acc:3819]
    ENSG00000076344 RGS11 regulator_of_G-protein_signaling_11_[Source:HGNC_Symbol;Acc:9993]
    ENSG00000174938 SEZ6L2 seizure_related_6_homolog_(mouse)-like_2_[Source:HGNC_Symbol;Acc:30844]
    ENSG00000122694 GLIPR2 GLI_pathogenesis-related_2_[Source:HGNC_Symbol;Acc:18007]
    ENSG00000167774 NDUFA7 NADH_dehydrogenase_(ubiquinone)1alpha_subcomplex,7,14.5kDa_[Source:HGNC_Symbol;Acc:7691]
    ENSG00000132164 SLC6A11 solute_carrier_family_6_(neurotransmitter_transporter,GABA),member_11_[Source:HGNC_Symbol;Acc:11044]

DAVID enrichment for DE genes

  • GW associated DE genes shared by cell types show no enrichment due to small gene lists.
  • GW15 vs GW 13: calcium ion binding in cortex UP and GE DN, neurogenesis in cortex DN.
  • GW17 vs GW 15: neurogenesis in GE, no enrichment in cortex.
  • GW17 vs GW 13: calcium ion binding in cortex UP and GE UP, neurogenesis in GE DN.

Isoform analysis

Sample DE_genes DE_exons with_expressed_genes isoform_exons exclude_DE_genes isoform_genes GW
Cortex-HuFNSC01_Cortex-HuFNSC03 565 28637 16045 8044 7772 2490 17 vs 15
Cortex-HuFNSC01_Cortex-HuFNSC04 530 27428 13200 6365 6134 2167 17 vs 13
Cortex-HuFNSC02_Cortex-HuFNSC03 681 28963 16765 7961 7630 2425 17 vs 15
Cortex-HuFNSC02_Cortex-HuFNSC04 722 29416 13894 6351 6011 2105 17 vs 13
Cortex-HuFNSC03_Cortex-HuFNSC04 642 26826 12185 5818 5479 1994 15 vs 13
GE-HuFNSC01_GE-HuFNSC03 861 31361 14725 5880 5458 2041 17 vs 15
GE-HuFNSC01_GE-HuFNSC04 883 34359 15889 6401 5996 2049 17 vs 13
GE-HuFNSC02_GE-HuFNSC03 921 32827 15557 5773 5306 1965 17 vs 15
GE-HuFNSC02_GE-HuFNSC04 869 34699 16012 6113 5711 1986 17 vs 13
GE-HuFNSC03_GE-HuFNSC04 545 24752 12223 4582 4422 1454 15 vs 13